A study of functional programming will demonstrate this untrue. The paragraph you quoted from the paper elaborates to specifically why references are complicated and low level: "introducing the concept of reference ... immediately gives rise in a high level language to one of the most notorious confusions of machine code, namely that between an address and its contents ... They cannot be input as data, and they cannot be output as results. If either data or references to data have to be stored on files or backing stores, the problems are immense". Perhaps one reason why people love working in JSON so much is because it only encodes values.
> indeed high level languages often move the other way, abandoning value types altogether
FP languages strongly emphasize programming with values. Rich Hickey, creator of Clojure programming language, gave an amazing talk "Simple made Easy" which is probably the best place to start to dive into this: http://www.infoq.com/presentations/Simple-Made-Easy